Chromatin immunoprecipitation (ChIP) is a powerful tool for evaluating interaction of proteins with specific genomic DNA regions in vivo, to provide a better understanding of the mechanisms of gene regulation, DNA replication, and DNA repair. The ChIP technique involves fixative treatment of live cells with formaldehyde to chemically cross-link DNA-bound proteins. The cells are then lysed, and the chromatin is sheared mechanically or enzymatically, in order to reduce fragment size and increase resolution. The resultant sheared complexes are then immuno-precipitated with antibodies specific to the protein of interest, and the DNA fragments are analyzed, e.g. using real time PCR, sequencing, or microarray hybridization. The ChIP protocol was introduced in 1988 (Solomon M J et al. Cell. 1988 53(6):937-47). Its power and widespread use has increased significantly with the incorporation of nucleic acid detection assays such as microarrays and sequencing that have enabled the method to be scaled genome-scale or genome-wide.